Agents Discussion

I agree with Dani's diminishing returns leveling process. So at the moment, we're pretty much in agreeance that, in terms of efficiency:

• Agents will begin at low efficiency, and you can level them up: each increase in efficiency becomes smaller as you progress.
  
• Organelle efficiency reductions simply limit how much of a compound the organelle can take in, making its production rate effectively decreased.
  

Now, my suggestions/answers.
On Plasmids:
Plasmids are (to my knowledge) only used by bacteria, and you won't be a bacteria in-game. Beyond this, as we've stated before, we don't want the game to be about running around and collecting parts- we want it to be about survival and more importantly reproduction. We do want a lush environment, but I think that can be achieved easily simply by having a high degree of biodiversity.

On Unlocking Agents
The Agent Vacuole evolves from a standard vacuole: you are granted the ability to use the vacuole randomly, but only if you already have a vacuole. When you add the Agent Vacuole, it gives you a random agent at low efficiency. From here, you can be granted (again, randomly) different types of agent which you can then manufacture in the vacuole (which will again begin at low efficiency): you can only manufacture one type of agent in a vacuole, so if you want to make 2 different types, you need 2 vacuoles, and so on.

I think I'll start making a CC doc for Agents.

I may not be a programmer but I agree that the limited leveling sounds good. As a gamer myself I can vouch for the mentality of "It's at 100% so I can just forget about it." Makes for a choice of, "Well, I can increase my agent's efficiency, or I can get something else that may make my cell survive better."

As for using vacuoles, what about the supply of them once they are made, with some a constant excretion would be better, such as the slime, but for others, what about storing them in the vacuole until they are needed, the size/shape of the vacuole would have some effect I would imagine. If that's a non-issue then never mind :lol:.

Seregon wrote:

A quick note about changing the 'efficiency' of an organelle, we can't arbitrarily change how much of an input is required to produce an output.  In photosynthesis, for example, you need 6 water (h2o) + 6 co2 to make 1 glucose (c6o6h12) + 6 oxygen (o2).  You can't increase efficiency by 50% and now produce 1 glucose + 6 oxygen per 4 water + 4 co2 (i.e.: 1.5 glucose per 6 water).  

Apart from being scientifically ridiculous, the main reason for this is that the compound system is supposed to be closed, it doesn't lose compounds, and they're not generated either, they're only converted from one form to another.

There are a few exceptions which we could play with.  One is energy input to the system (light + heat), so that we could make chloroplasts/thermoplasts use more or less light/heat in order to produce sugar.  The other is stored energy (ATP) used/produced by various processes, as for most processes the energy requirements is arbitrarily chosen by us (we simply don't know the true values), and even where we do know (aerobic respiration) we have a range of possible values (32-38 ATP per glucose?) and we can reasonably say that primitive aerobic respiration produced less (and more advanced versions may produce a little more).

Effectively, changes in process efficiency (due to either agents or upgrades to organelles) can change the rate at which they occur, and the amount of energy they produce/use, but not the amount of input/output compounds they require/produce, if we want to keep this scientific.

So agents would affect the processing power of organelles, or their efficiency when the input is specifically some sort of energy like light, heat or ATP.

I agree on the idea of the compound system being a closed system, but isn't that impossible to avoid? When a cell converts a compound to ATP, and then uses that ATP to move, isn't the ATP expended and not converted? (Nevermind I completely forgot one of the basics of biology). For later stages in the game, such as the Strategy Mode, when your population consumes a certain mass of food, it just gets consumed and does not turn into anything. I guess this means we should introduce waste production system to keep the balance of compounds.

NickTheNick wrote:

Seregon wrote:

A quick note about changing the 'efficiency' of an organelle, we can't arbitrarily change how much of an input is required to produce an output.  In photosynthesis, for example, you need 6 water (h2o) + 6 co2 to make 1 glucose (c6o6h12) + 6 oxygen (o2).  You can't increase efficiency by 50% and now produce 1 glucose + 6 oxygen per 4 water + 4 co2 (i.e.: 1.5 glucose per 6 water).  

Apart from being scientifically ridiculous, the main reason for this is that the compound system is supposed to be closed, it doesn't lose compounds, and they're not generated either, they're only converted from one form to another.

There are a few exceptions which we could play with.  One is energy input to the system (light + heat), so that we could make chloroplasts/thermoplasts use more or less light/heat in order to produce sugar.  The other is stored energy (ATP) used/produced by various processes, as for most processes the energy requirements is arbitrarily chosen by us (we simply don't know the true values), and even where we do know (aerobic respiration) we have a range of possible values (32-38 ATP per glucose?) and we can reasonably say that primitive aerobic respiration produced less (and more advanced versions may produce a little more).

Effectively, changes in process efficiency (due to either agents or upgrades to organelles) can change the rate at which they occur, and the amount of energy they produce/use, but not the amount of input/output compounds they require/produce, if we want to keep this scientific.

So agents would affect the processing power of organelles, or their efficiency when the input is specifically some sort of energy like light, heat or ATP.

I agree on the idea of the compound system being a closed system, but isn't that impossible to avoid? When a cell converts a compound to ATP, and then uses that ATP to move, isn't the ATP expended and not converted? (Nevermind I completely forgot one of the basics of biology). For later stages in the game, such as the Strategy Mode, when your population consumes a certain mass of food, it just gets consumed and does not turn into anything. I guess this means we should introduce waste production system to keep the balance of compounds.

Strat mode can be a lot less confined/OT

Yes, there are a few places where we need to be careful about the system being closed or not. ATP for example is really made from ADP + phosphate, and when used is converted back to those, but there's really no point modelling that in the game. Basically, the only thing that should leak from the system (in the early stages) is ATP, and the only thing that should be added is light/heat energy.

For the later stages, as scio said, we don't need to be so strict. However, if we want a closed system (there are advantages, but I don't yet know if it's necessary), we would need to model waste. In your food example, that food would be converted to a mix of sewage and atmospheric gases when consumed, and we would probably put the nutrients in the sewage directly back into the environment as soil nutrients... unless we want to properly simulate fertility.

Seregon wrote:

Yes, there are a few places where we need to be careful about the system being closed or not.  ATP for example is really made from ADP + phosphate, and when used is converted back to those, but there's really no point modelling that in the game.  Basically, the only thing that should leak from the system (in the early stages) is ATP, and the only thing that should be added is light/heat energy.

Actually, we do have an exit when compound clouds fade out. That could present a problem. One workaround I can see is having background compound levels, where no matter where you are, the concentrations of compounds are at some constant low base.

For the upgrade system, I think we should use levels as described by the sequence
a_n=a_n-1+(13-n) 
where
a₀=22
We then get the sequence
22,34,45,55,64,72,79,85,90,94,97,98,100

Assuming that all agents are made from some mixture of compounds (otherwise they would be pure energy and we don't need to worry about it), when they break down/dissipate we can return those compounds to the overall environment, and they would be averaged over the environments area to give the back ground levels you suggest.  The same background level would apply to other ubiquitous compounds such as dissolved oxygen/co2 etc.

EDIT - just realised your post was compound clouds in general, not agents specifically, so what you said is pretty much what i would've suggested.

Seregon wrote:

Assuming that all agents are made from some mixture of compounds (otherwise they would be pure energy and we don't need to worry about it), when they break down/dissipate we can return those compounds to the overall environment, and they would be averaged over the environments area to give the back ground levels you suggest.  The same background level would apply to other ubiquitous compounds such as dissolved oxygen/co2 etc.

EDIT - just realised your post was compound clouds in general, not agents specifically, so what you said is pretty much what i would've suggested.

Ok, glad we got that figured out, otherwise we'd have serious ecological issues. Also, what do we want to make agents out of, and how much energy does it take to make them. I'm going to say right away that I want all agents to be made of the exact same ingredients to save us a whole lot of work down the line.
I'm going to say we make agents out of a little bit of everything.
_Protein
+_H₂O
+_Sugar
+_Fat
___________
= 1 Compound
I'm just going to take a shot in the dark and say
 3 Protein
+6 H₂O
+6 Sugar
+2 Fat

Pretty much agree with that. Definately have them all made of the same thing, primarily protein and some sugar, not sure if they'd need fat or water.

At this point we could have them made of a bit of everything as you say, but in terms of gameplay we might want to consider having different basic compounds (protein, sugar, fat) be useful for different things:
sugar -> energy, signalling molecules (that's a guess, I know they're used for cell surface receptors)
fat -> energy, cell membranes and organelle construction
protein -> agents, flagella and other structures, organelle construction...

Seregon wrote:

Pretty much agree with that.  Definately have them all made of the same thing, primarily protein and some sugar, not sure if they'd need fat or water.

At this point we could have them made of a bit of everything as you say, but in terms of gameplay we might want to consider having different basic compounds (protein, sugar, fat) be useful for different things:
sugar -> energy, signalling molecules (that's a guess, I know they're used for cell surface receptors)
fat -> energy, cell membranes and organelle construction
protein -> agents, flagella and other structures, organelle construction...

That's something more for a general compound management thread.
I put the water drain in to account for dehydration synthesis. I'd like to have signal agents be made purely of sugar for realism, but I don't know if it's really worth doing at all, so at this point, we say all agents are made of the same thing.

Dehidratation? All the microbe stage will be inside a water environement, composed roughly of 99% water, so i dont think any microbe will have problems with that.

Making them out of compounds and releasing the compounds back seems good to me.

However, i dont like your formula, scio. That makes upgrade level 13 be the top one, while the goal of my proposal was to not have a top upgrade level.
Edit: For the upgrades, i mean.

Daniferrito wrote:

Dehidratation? All the microbe stage will be inside a water environement, composed roughly of 99% water, so i dont think any microbe will have problems with that.

Making them out of compounds and releasing the compounds back seems good to me.

However, i dont like your formula, scio. That makes upgrade level 13 be the top one, while the goal of my proposal was to not have a top upgrade level.
Edit: For the upgrades, i mean.

Ok, I can try to rework something geometric for you.
Dehydration synthesis is the use of water to bond chemicals together.

Agree that this is getting a little off topic. I looked up dehydration synthesis, and it's the reagents which get dehydrated, so that water is one of the outputs, not inputs. I would treat signalling agents seperately to other agents, if we have them at all, but thats a discussion for later on, when we get to early multicellular perhaps?

Ok, sorry. I should have knew it, or at least searched it, but i didnt saw it. Thats probably a good sign that i should go to bed for today.

~sciocont wrote:

Daniferrito wrote:

Dehidratation? All the microbe stage will be inside a water environement, composed roughly of 99% water, so i dont think any microbe will have problems with that.

Making them out of compounds and releasing the compounds back seems good to me.

However, i dont like your formula, scio. That makes upgrade level 13 be the top one, while the goal of my proposal was to not have a top upgrade level.
Edit: For the upgrades, i mean.

Ok, I can try to rework something geometric for you.
Dehydration synthesis is the use of water to bond chemicals together.

From my understanding Dani is going for an infinite geometric series, which technically does have a limit but has an infinite number of increments, aka "Levels", which I think is a good idea.

Lol, i didnt saw that part of the post even.

Yes, my sugestion is a serie that has a limit of 100 or less, but that its infinite. It doesent need to be geometric, though, as long as it behaves the way we want, it is good. Actually, the shape i like the most would be logaritmic, but that one doesent have a finite limit.

The simplest equation would be something similair to the logistic function, which is basicaly logarithmic:

Eff = 1 - 1 / a^n

where 'n' is the upgrade step (1,2,3...) and 'a' is a tweaking parameter somewhere between 1 and 2.

a = 2 gives us the sequence on the previous page:

Spoiler:

and a = 1.1 gives us something more gradual:

Spoiler:

or in graph form, the bottom green line is for a=1.1, the top line is a=2, the others are in 0.1 increments:

Spoiler:

trying to work out an equation with a fixed starting efficiency now...

I'd take the 1.2 model there. Starts off fairly low and has a gradual gain
I believe you meant to say "Eff = 1 - (1 / a^n)"

If you figure the starting point out, I'd like to see a start at around 15-20 percent. I'll play with it and see if I can get a set start equation as well, but my money is on you.

Yup, that's what I meant, fixed it.

Literally just figured something out as you posted that, it's not as neat as the original, but it works:

Eff = 1 - (1-s) * a^(1-n)

or (same equation, but looks more similair to the previous post)

Eff = 1 - (1-s) * (a / a^n)

where 'a' and 'n' are as above, and 's' is the starting point.

The lines are the same 'a' values as above, the horizontal blue one is a=1.  Starting point s=0.2

Spoiler:

I would agree that somewhere around a = 1.2 to 1.4 looks pretty good.

EDIT:

~sciocont wrote:

...but my money is on you.

I had a bit of a head start... you may be able to make some improvement on what I came up with though, I think theres something simpler out there, but it'll do for now. I'm going to leave it at that for tonight, and get some sleep...

Nice work.
I'm actually looking at the equation with a start point of .15 (.1 seemed too low)
eff= 1 - (1-.15)*(1.25^1-n)
Which gives
1=>.15
2=>.32
3=>.456
4=>.5648
5=>.6518
6=>.7215
7=>.7772
8=>.8217
9=>.8574
10=>.8859
11=>.9087
Which I think is very nice.

That looks quite good. A slight note, through:

Eff = l - (l-s) * a^(1-n)

Where:
l - Limit. The point it ends at, in case we decide to lower that value.
s - Starting point. What f[1] is.
a - How fast does it grow. Higher values make it grow faster

I just added the limit.
The values sugested by scio (and i agree) are:
l - Either 1 or 100, depending if we express the percentage over 1 or over 100%
s - .15
a - 1.25

Finally:

Eff = l - (l-s) * a^(-n)

Thats just the exact same function "shifted" one node to the left. That would make f[0] = s, how eficient it is when it has no upgrades yet. But thats just tecnicalism.

Ok, our efficiency woes have been answered. What else needs to be completed?

Now we need to come up with a list of possible effects an agent can have. I think you listed some on the first page.

Slime: Reduces movement speed
Agent destroying enzyme/Anti-Agent: Eliminates other agents

Here are some others that I remember earlier mentioned but yet to be listed on this thread:

Organelle Contaminant: Reduces processing power or efficiency of targeted organelles.
Signalling Agents: Sends a message to target cells (Repel cells, warn cells, etc.)

This list is very bare, I will need some help remembering what was discussed.

I think the discussion veered towards discussing the efficiency of the agents and the vacuoles rather than a list of possible effects. I do have two ideas

• Calcifying/Petrifying Agent: Cells can’t move at all on their own, will still drift (disables movement organelles like flagella and cilia)
• Anti-Membrane Agent: Attacks the membranes of other cells, constant damage until it bursts, releasing the compounds held within.

Immortal_Dragon wrote:

• Calcifying/Petrifying Agent: Cells can’t move at all on their own, will still drift (disables movement organelles like flagella and cilia)

Isn't that just an organelle contaminant with 100% processing power reduction?